2023
The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics
Huang X, Gan Z, Cui H, Lan T, Liu Y, Caron E, Shao W. The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics. Nucleic Acids Research 2023, 52: d1062-d1071. PMID: 38000392, PMCID: PMC10767952, DOI: 10.1093/nar/gkad1068.Peer-Reviewed Original ResearchUnlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery
Stutzmann C, Peng J, Wu Z, Savoie C, Sirois I, Thibault P, Wheeler A, Caron E. Unlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery. Cell Reports Methods 2023, 3: 100511. PMID: 37426761, PMCID: PMC10326451, DOI: 10.1016/j.crmeth.2023.100511.Peer-Reviewed Original ResearchMeSH KeywordsAntigens, NeoplasmHistocompatibility Antigens Class IHLA AntigensHumansMass SpectrometryMicrofluidicsNeoplasmsConceptsSingle-cell proteomicsMicrofluidic technologyPotential of microfluidicsMass spectrometrySample preparationDroplet microfluidicsDigital microfluidicsMicrofluidic methodPhysical moleculesMicrofluidicsHigh sensitivityReproducible mannerPillar arraysRecent advancesSpectrometryMoleculesImmunopeptidomicsPowerful toolProteomicsPreparationMSPeptidesSolution
2021
Generation of HLA Allele-Specific Spectral Libraries to Identify and Quantify Immunopeptidomes by SWATH/DIA-MS
Kovalchik K, Hamelin D, Caron E. Generation of HLA Allele-Specific Spectral Libraries to Identify and Quantify Immunopeptidomes by SWATH/DIA-MS. Methods In Molecular Biology 2021, 2420: 137-147. PMID: 34905171, DOI: 10.1007/978-1-0716-1936-0_11.Peer-Reviewed Original ResearchRHybridFinder: An R package to process immunopeptidomic data for putative hybrid peptide discovery
Saab F, Hamelin D, Ma Q, Kovalchik K, Sirois I, Faridi P, Li C, Purcell A, Kubiniok P, Caron E. RHybridFinder: An R package to process immunopeptidomic data for putative hybrid peptide discovery. STAR Protocols 2021, 2: 100875. PMID: 34746858, PMCID: PMC8551247, DOI: 10.1016/j.xpro.2021.100875.Peer-Reviewed Original ResearchImmunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis.
Sirois I, Isabelle M, Duquette J, Saab F, Caron E. Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis. Journal Of Visualized Experiments 2021 PMID: 34723952, DOI: 10.3791/63052.Peer-Reviewed Original ResearchConceptsImmunopeptidomics workflowsComposition of peptidesSample preparation procedureQuality control samplesMass spectrometry analysisPreparation procedureElution efficiencySample preparationSpectrometry analysisPeptidesImmunoaffinity purificationReagentsMoleculesComplexesPreparationPurificationStepMHC-peptide complexesControl samplesImmunopeptidomicsNew protocolReproducibilityEfficiencyBeadsTechnology platform
2020
The SysteMHC Atlas: a Computational Pipeline, a Website, and a Data Repository for Immunopeptidomic Analyses
Shao W, Caron E, Pedrioli P, Aebersold R. The SysteMHC Atlas: a Computational Pipeline, a Website, and a Data Repository for Immunopeptidomic Analyses. Methods In Molecular Biology 2020, 2120: 173-181. PMID: 32124319, DOI: 10.1007/978-1-0716-0327-7_12.Peer-Reviewed Original Research
2019
The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases*
Vizcaíno J, Kubiniok P, Kovalchik K, Ma Q, Duquette J, Mongrain I, Deutsch E, Peters B, Sette A, Sirois I, Caron E. The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases*. Molecular & Cellular Proteomics 2019, 19: 31-49. PMID: 31744855, PMCID: PMC6944237, DOI: 10.1074/mcp.r119.001743.Peer-Reviewed Original Research
2018
A tissue-based draft map of the murine MHC class I immunopeptidome
Schuster H, Shao W, Weiss T, Pedrioli P, Roth P, Weller M, Campbell D, Deutsch E, Moritz R, Planz O, Rammensee H, Aebersold R, Caron E. A tissue-based draft map of the murine MHC class I immunopeptidome. Scientific Data 2018, 5: 180157. PMID: 30084848, PMCID: PMC6080492, DOI: 10.1038/sdata.2018.157.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsHistocompatibility Antigens Class IMass SpectrometryMiceMice, Inbred C57BLOrgan SpecificityPeptidesConceptsMHC class IClass IMurine MHC class IPotential tumor-associated antigenMajor histocompatibility complex class IHistocompatibility complex class ITumor-associated antigensComplex class IC57BL/6 miceT cellsTranslational immunologyCancer modelImmune systemNormal tissuesMS injectionMost tissuesTissueInitial qualitative dataTotal numberPeptidesCD8AtlasAntigenMice
2017
Deciphering the MHC-associated peptidome: a review of naturally processed ligand data
Vaughan K, Xu X, Caron E, Peters B, Sette A. Deciphering the MHC-associated peptidome: a review of naturally processed ligand data. Expert Review Of Proteomics 2017, 14: 729-736. PMID: 28756714, DOI: 10.1080/14789450.2017.1361825.Peer-Reviewed Original ResearchA Case for a Human Immuno-Peptidome Project Consortium
Caron E, Aebersold R, Banaei-Esfahani A, Chong C, Bassani-Sternberg M. A Case for a Human Immuno-Peptidome Project Consortium. Immunity 2017, 47: 203-208. PMID: 28813649, DOI: 10.1016/j.immuni.2017.07.010.Peer-Reviewed Original ResearchPrecise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry
Caron E, Roncagalli R, Hase T, Wolski W, Choi M, Menoita M, Durand S, García-Blesa A, Fierro-Monti I, Sajic T, Heusel M, Weiss T, Malissen M, Schlapbach R, Collins B, Ghosh S, Kitano H, Aebersold R, Malissen B, Gstaiger M. Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry. Cell Reports 2017, 18: 3219-3226. PMID: 28355572, PMCID: PMC5382234, DOI: 10.1016/j.celrep.2017.03.019.Peer-Reviewed Original ResearchConceptsSWATH mass spectrometryProtein interactionsProtein interaction dynamicsPrimary cellsTissue-specific contextDifferential protein expressionCell-signaling eventsInteraction proteomeProtein Grb2Cellular functionsMouse geneticsCell signalingAffinity purificationMammalian tissuesDevelopmental stagesTemporal profilingSpatiotemporal organizationMass spectrometryFundamental processesProtein expressionCell populationsRobust workflowCellsInteraction dynamicsGrb2
2016
Contribution of Mass Spectrometry-Based Proteomics to the Understanding of TNF‑α Signaling
Ciuffa R, Caron E, Leitner A, Uliana F, Gstaiger M, Aebersold R. Contribution of Mass Spectrometry-Based Proteomics to the Understanding of TNF‑α Signaling. Journal Of Proteome Research 2016, 16: 14-33. PMID: 27762135, DOI: 10.1021/acs.jproteome.6b00728.Peer-Reviewed Original ResearchConceptsTNF-α signalingProteomics researchDimeric transcription factorsComplex signaling cascadesSystems-level understandingProteome levelProteomic landscapeCellular processesTranscription factorsSignaling cascadesNF-κBSignalingLevel understandingMass spectrometryProteomeActivationProteomicsSpite of decadesCytokines IL-1βDifferentiationLimited knowledgePathwayCascadeFamilyTNF
2015
An open-source computational and data resource to analyze digital maps of immunopeptidomes
Caron E, Espona L, Kowalewski D, Schuster H, Ternette N, Alpízar A, Schittenhelm R, Ramarathinam S, Arlehamn C, Koh C, Gillet L, Rabsteyn A, Navarro P, Kim S, Lam H, Sturm T, Marcilla M, Sette A, Campbell D, Deutsch E, Moritz R, Purcell A, Rammensee H, Stevanovic S, Aebersold R. An open-source computational and data resource to analyze digital maps of immunopeptidomes. ELife 2015, 4: e07661. PMID: 26154972, PMCID: PMC4507788, DOI: 10.7554/elife.07661.Peer-Reviewed Original ResearchMeSH KeywordsAntigen PresentationAntigensComputational BiologyDatabases, FactualHigh-Throughput Screening AssaysHLA AntigensMass SpectrometryPeptides
2014
A repository of assays to quantify 10,000 human proteins by SWATH-MS
Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R. A repository of assays to quantify 10,000 human proteins by SWATH-MS. Scientific Data 2014, 1: 140031. PMID: 25977788, PMCID: PMC4322573, DOI: 10.1038/sdata.2014.31.Peer-Reviewed Original Research
2011
The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation
Caron E, Vincent K, Fortier M, Laverdure J, Bramoullé A, Hardy M, Voisin G, Roux P, Lemieux S, Thibault P, Perreault C. The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation. Molecular Systems Biology 2011, 7: msb201168. PMID: 21952136, PMCID: PMC3202804, DOI: 10.1038/msb.2011.68.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCD8-Positive T-LymphocytesCell Line, TumorCell MembraneGene Expression ProfilingHigh-Throughput Screening AssaysHistocompatibility Antigens Class IImmunityMajor Histocompatibility ComplexMass SpectrometryMetabolic Networks and PathwaysMiceOligonucleotide Array Sequence AnalysisPeptidesProteomicsSignal TransductionSirolimusSystems BiologyTandem Mass SpectrometryTOR Serine-Threonine KinasesConceptsCell surfaceMass spectrometry-based approachSystems-level evidenceSelf/non-self discriminationCellular regulationPredictive biologyCellular metabolic activityCellular metabolismNon-self discriminationRapamycin resultsMammalian targetMHC IBiochemical networksCD8 T lymphocytesSystems immunologyMajor histocompatibility complex (MHC) class I moleculesMetabolic eventsExtrinsic factorsMetabolic activityIntegrative viewClass I moleculesImmunotherapeutic interventionsT lymphocytesEssence of selfSystem-level perspective